Variant annotation using VEP

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2.7 years ago

nkausthu ▴ 30

Hi,

I am annotating the variants using VEP to get an output as tab format file. But I am not getting the details of 'INFO' columns, such as Zygosity, Read Number and Read frequencies. It would be great if someone can help me to figure this out. Thanks in advance.

Annotation Zygosity VEP • 988 views

ADD COMMENT • link updated 2.5 years ago by smrutimayipanda ▴ 20 • written 2.7 years ago by nkausthu ▴ 30

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You can save your output in VCF format or you can use this plugin to do the task.

ADD REPLY • link 2.7 years ago by brunobsouzaa ▴ 830

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Thank you for the reply. Again in the end we need use awk and parse the output accordingly.

ADD REPLY • link 2.7 years ago by nkausthu ▴ 30

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I want the columns of zygosity, variant reads, reads frequencies and variant coverage from VEP. How to get that? Please anyone tell me

ADD REPLY • link 2.5 years ago by smrutimayipanda ▴ 20

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